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- PDB-5jk8: Phenylalanine hydroxylase from dictyostelium - BH2, norleucine complex -

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Basic information

Entry
Database: PDB / ID: 5jk8
TitlePhenylalanine hydroxylase from dictyostelium - BH2, norleucine complex
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / Phenylalanine hydroxylase / Dictyostelium / enzyme regulation / tetrahydrobiopterin
Function / homology
Function and homology information


Catecholamine biosynthesis / Serotonin and melatonin biosynthesis / Phenylalanine metabolism / prephenate dehydratase activity / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / asexual reproduction / phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process ...Catecholamine biosynthesis / Serotonin and melatonin biosynthesis / Phenylalanine metabolism / prephenate dehydratase activity / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / asexual reproduction / phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / tyrosine biosynthetic process / L-phenylalanine biosynthetic process / L-phenylalanine catabolic process / tetrahydrobiopterin binding / iron ion binding / identical protein binding
Similarity search - Function
Prephenate dehydratase, conserved site / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily ...Prephenate dehydratase, conserved site / Eukaryotic phenylalanine-4-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase / Biopterin-dependent aromatic amino acid hydroxylase family profile. / ACT domain profile. / ACT domain / ACT-like domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 7,8-DIHYDROBIOPTERIN / NORLEUCINE / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.394 Å
AuthorsZhuang, N. / Lee, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National research foundation Korea, Republic Of
CitationJournal: To Be Published
Title: Phenylalanine hydroxylase from dictyostelium - BH2, norleucine complex
Authors: Zhuang, N. / Lee, K.H.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanine-4-hydroxylase
B: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55510
Polymers100,0982
Non-polymers1,4578
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-34 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.516, 85.668, 73.482
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phenylalanine-4-hydroxylase / PAH / Phe-4-monooxygenase / Tryptophan 5-hydroxylase / TRH / Tryptophan 5-monooxygenase


Mass: 50049.023 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: pah, DDB_G0278781 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q54XS1, phenylalanine 4-monooxygenase, tryptophan 5-monooxygenase

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#3: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N5O3
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NLE / NORLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 26%(w/v) PEG 2000, 0.06 M PIPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 32512 / % possible obs: 98.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
Cootmodel building
RefinementResolution: 2.394→34.742 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 27.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 1648 5.07 %Random
Rwork0.1649 ---
obs0.1689 32511 98.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.394→34.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6223 0 90 61 6374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086484
X-RAY DIFFRACTIONf_angle_d1.0998804
X-RAY DIFFRACTIONf_dihedral_angle_d15.5222443
X-RAY DIFFRACTIONf_chiral_restr0.043942
X-RAY DIFFRACTIONf_plane_restr0.0061138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3936-2.46410.29441390.23322507X-RAY DIFFRACTION97
2.4641-2.54360.31981470.21772589X-RAY DIFFRACTION100
2.5436-2.63450.31941290.20982581X-RAY DIFFRACTION100
2.6345-2.73990.30841470.21372588X-RAY DIFFRACTION100
2.7399-2.86450.30631420.20722592X-RAY DIFFRACTION100
2.8645-3.01550.24911200.19622585X-RAY DIFFRACTION100
3.0155-3.20430.2861400.20812616X-RAY DIFFRACTION100
3.2043-3.45150.2891150.19312601X-RAY DIFFRACTION100
3.4515-3.79840.23731490.16782598X-RAY DIFFRACTION100
3.7984-4.34720.22621360.14452591X-RAY DIFFRACTION99
4.3472-5.47350.20121360.13512598X-RAY DIFFRACTION98
5.4735-34.74570.21711480.13772417X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4050.9693-0.07912.6489-0.77682.30350.13380.38870.2294-0.36920.19610.32470.1157-0.2852-0.29160.47210.0129-0.00590.38790.00580.478339.28590.94239.6912
24.09280.97540.18782.6726-0.88172.70190.0885-0.4250.03570.4104-0.0433-0.0142-0.0666-0.1923-0.01960.44210.0051-0.02370.4369-0.00310.399648.9237-3.639342.0202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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